# run in terminal:
# sudo apt install cmake libgdal-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev libmagick++-dev libfftw3-dev

# basic R
install.packages(c("tidyverse", "BiocManager", "data.table", "DT", "remotes", "devtools", "librarian"), Ncpus = 6)

# survival analysis
install.packages("survminer", Ncpus = 6)

# cytometry
BiocManager::install(c("RGLab/cytoinstaller", "COMPASS", "DillonHammill/CytoExploreRData", "DillonHammill/CytoExploreR"), Ncpus = 6)

# bulk RNA
BiocManager::install(c("DESeq2", "edgeR", "tidybulk", "tidySummarizedExperiment"), Ncpus = 6)

# single cell
# some version of ggtree will conflict with ggplot2
# try remotes::install_github("YuLab-SMU/ggtree")
BiocManager::install(c("Seurat", "tidyseurat", "clusterProfiler", "singleCellTK", "SingleR", "celldex", "harmony", "enrichR", "SoupX"), Ncpus = 6)

# genetics
install.packages(c("hierfstat", "LDlinkR", "snpStats"), Ncpus = 6)
remotes::install_url("https://cran.r-project.org/src/contrib/Archive/LDheatmap/LDheatmap_1.0-6.tar.gz")
